From b5143c79de268b844f3a6a63d92c6389b047f35e Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 9 Nov 2020 16:55:33 -0500
Subject: Make it so "pangenome analysis" only runs collect-seqs.

Will ensure that metadata is kept up to date.

GFA isn't being generated.  Will introduce new workflow that uses
from_sparql to analyze a subset.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 bh20seqanalyzer/main.py                       | 2 +-
 bh20simplewebuploader/templates/resource.html | 4 ++--
 workflows/update-workflows.sh                 | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 5f00080..0906958 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -215,7 +215,7 @@ class SeqAnalyzer:
         most_recent_analysis = self.api.groups().list(filters=[['owner_uuid', '=', self.pangenome_analysis_project]],
                                                       order="created_at desc").execute()
         for m in most_recent_analysis["items"]:
-            wf = self.get_workflow_output_from_project(m["uuid"], "arv-main.cwl")
+            wf = self.get_workflow_output_from_project(m["uuid"], "collect-seqs.cwl")
             if wf is None:
                 continue
             src = self.api.collections().get(uuid=wf["output_uuid"]).execute()
diff --git a/bh20simplewebuploader/templates/resource.html b/bh20simplewebuploader/templates/resource.html
index fc52f13..4c50fb9 100644
--- a/bh20simplewebuploader/templates/resource.html
+++ b/bh20simplewebuploader/templates/resource.html
@@ -10,8 +10,8 @@
 	<p><a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-5ct8p1i1wrgyjvp#Data_collections">All sequences project</a></p>
 	<p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.fasta">All sequences (FASTA) relabled and deduplicated</a></p>
 	<p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">Metadata (RDF) for all sequences</a></p>
-	<p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.gfa">All sequences in Graphical Fragment Assembly (GFA)</a> - <a href="https://github.com/GFA-spec/GFA-spec">More about GFA</a></p>
-	<p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.unchop.sorted.odgi">All sequences in Optimized Dynamic Genome/Graph Implementation (ODGI)</a> - <a href="https://github.com/vgteam/odgi">More about ODGI</a></p>
+	<!-- <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.gfa">All sequences in Graphical Fragment Assembly (GFA)</a> - <a href="https://github.com/GFA-spec/GFA-spec">More about GFA</a></p> -->
+	<!-- <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.unchop.sorted.odgi">All sequences in Optimized Dynamic Genome/Graph Implementation (ODGI)</a> - <a href="https://github.com/vgteam/odgi">More about ODGI</a></p> -->
 	<!-- <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.ttl.xz">All sequences in RDF using spodgi</a> - <a href="https://github.com/pangenome/spodgi">More about spodgi</a></p> -->
 
 
diff --git a/workflows/update-workflows.sh b/workflows/update-workflows.sh
index 3b69a58..5182ec4 100755
--- a/workflows/update-workflows.sh
+++ b/workflows/update-workflows.sh
@@ -1,3 +1,3 @@
 #!/bin/sh
 arvados-cwl-runner --project-uuid=lugli-j7d0g-5hswinmpyho8dju --update-workflow=lugli-7fd4e-2zp9q4jo5xpif9y fastq2fasta/fastq2fasta.cwl
-arvados-cwl-runner --project-uuid=lugli-j7d0g-5hswinmpyho8dju --update-workflow=lugli-7fd4e-mqfu9y3ofnpnho1 pangenome-generate/arv-main.cwl
+arvados-cwl-runner --project-uuid=lugli-j7d0g-5hswinmpyho8dju --update-workflow=lugli-7fd4e-mqfu9y3ofnpnho1 pangenome-generate/collect-seqs.cwl
-- 
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